- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 57f023: Remove tool form mako
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 57f023529aef13723cb1555dc3ad5ea59aef009c https://github.com/galaxyproject/galaxy/commit/57f023529aef13723cb1555dc3ad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form.js R templates/webapps/galaxy/tool_form.mako M test/unit/tools/test_execution.py Log Message: ----------- Remove tool form mako Fix new-line Commit: f5a6e25ebd9d96a709781291cf04bc9e461216c6 https://github.com/galaxyproject/galaxy/commit/f5a6e25ebd9d96a709781291cf04… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Reinsert data_source tool execution into tool runner controller (requires separate PR) Commit: c1faf48d819ded4317995fe5f5ca436f847a4d09 https://github.com/galaxyproject/galaxy/commit/c1faf48d819ded4317995fe5f5ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add large message style and use for initial tool loading notifications Commit: 7777ea8f91928a9dd2c581eed53ba7e2ed1f3255 https://github.com/galaxyproject/galaxy/commit/7777ea8f91928a9dd2c581eed53b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Extend large ui-messages to cover states (info, warning, danger, success) Commit: 6d00f38f0a08281d5597872616154af0b3d306c2 https://github.com/galaxyproject/galaxy/commit/6d00f38f0a08281d559787261615… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M .gitignore M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/run.py M lib/pulsar/client/amqp_exchange.py M scripts/common_startup.sh M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/tools/tools-jobs.js A test-data/1.RData M test/api/helpers.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/test_data.py M test/base/twilltestcase.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_parsing.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_003 Conflicts: client/galaxy/scripts/mvc/tools/tools-form.js static/maps/mvc/tools/tools-form.js.map static/scripts/mvc/tools/tools-form.js Commit: 082c8952e03d11a44bd0cd354a3560f2471305e0 https://github.com/galaxyproject/galaxy/commit/082c8952e03d11a44bd0cd354a35… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Undo initial errors Commit: 728c5450906c8b2ba395f06fa4dbe7e7cc5a7aa6 https://github.com/galaxyproject/galaxy/commit/728c5450906c8b2ba395f06fa4db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/tools.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/tools.js Log Message: ----------- Hide regular tool form for upload tool Commit: 6ee9a08cf2d3624985ceed2cf4f4bfd46ca24563 https://github.com/galaxyproject/galaxy/commit/6ee9a08cf2d3624985ceed2cf4f4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/ui/ui-misc.js R templates/webapps/galaxy/tool_form.mako M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #786 from guerler/tool_form_003 Remove tool form mako, reduce tool runner, fix job resubmission options Compare: https://github.com/galaxyproject/galaxy/compare/b1a8aebad680...6ee9a08cf2d3

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[galaxyproject/galaxy] 1a13ef: API, Datasets: fix returned tuple from creating_jo...
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a13efe488037aa30a98c80fdab8287bfdaaf923 https://github.com/galaxyproject/galaxy/commit/1a13efe488037aa30a98c80fdab8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py Log Message: ----------- API, Datasets: fix returned tuple from creating_job; normalize id encoding, parens, naming; move both rerunnable and creating_job into datasets.py to allow (future?) use by lddas and ldas Commit: b1a8aebad680654bb2c9f19fe4b126e7fb3def2f https://github.com/galaxyproject/galaxy/commit/b1a8aebad680654bb2c9f19fe4b1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py Log Message: ----------- Merge pull request #817 from carlfeberhard/fix.creating_job API, Datasets: fix returned tuple from creating_job Compare: https://github.com/galaxyproject/galaxy/compare/9aee2122251c...b1a8aebad680

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[galaxyproject/galaxy] 8a30d3: Fix change_password (destination for password rese...
by GitHub 29 Sep '15

29 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 8a30d3add42904f1117599790d63dfa273374d51 https://github.com/galaxyproject/galaxy/commit/8a30d3add42904f1117599790d63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix change_password (destination for password reset link) to work w/ require_login Commit: 76fcde3274688db10eb259cdf25dbcc0d5187262 https://github.com/galaxyproject/galaxy/commit/76fcde3274688db10eb259cdf25d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #811 from dannon/prt_fix [15.07] Fix change_password (destination for password reset link) to work w/ … Compare: https://github.com/galaxyproject/galaxy/compare/8c9e8686a159...76fcde327468

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[galaxyproject/galaxy] 030624: expose lib create time; show error message when de...
by GitHub 29 Sep '15

29 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03062478a9c381514a61240f25f54681f3cc733c https://github.com/galaxyproject/galaxy/commit/03062478a9c381514a61240f25f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- expose lib create time; show error message when deleting folders Commit: bab1e3b562814c4091200e27ff579c6c54502a13 https://github.com/galaxyproject/galaxy/commit/bab1e3b562814c4091200e27ff57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py Log Message: ----------- add update method to folder manager; update root folder name when lib name is updated; refactor exception imports Commit: b28810444d60dabccee8239a8bff0febc3fc8876 https://github.com/galaxyproject/galaxy/commit/b28810444d60dabccee8239a8bff… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- expose API to update lib folder; make manager not update when nothing changes Commit: 796f803df0bc139b7ae3d1f7cf6d718da186cef7 https://github.com/galaxyproject/galaxy/commit/796f803df0bc139b7ae3d1f7cf6d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M lib/galaxy/managers/folders.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- provide UI to delete and udelete lib folders; slight refactor Commit: 10c915bb62c69017a6cf7ffc18a90f196899feb9 https://github.com/galaxyproject/galaxy/commit/10c915bb62c69017a6cf7ffc18a9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M .gitignore M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/grunt-tasks/scripts.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/workflow/run.py M scripts/common_startup.sh M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/upload-row.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/upload-row.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js A test-data/1.RData M test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/test_data.py M test/base/twilltestcase.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/unit/jobs/test_job_configuration.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge branch 'dev' into data-lib-work Conflicts: static/maps/mvc/library/library-foldertoolbar-view.js.map static/scripts/mvc/library/library-foldertoolbar-view.js also re-grunted Commit: b77c28cd77fa4ccfb37e2ac8feceba5dc1628ffb https://github.com/galaxyproject/galaxy/commit/b77c28cd77fa4ccfb37e2ac8fece… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py Log Message: ----------- flake8 fix Commit: f778a3864c8d95ea91359de7cc3f44dc78a290d1 https://github.com/galaxyproject/galaxy/commit/f778a3864c8d95ea91359de7cc3f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- :bird::eyes: and some docs Commit: e9f12d3b5b297b52372dbbf23a45955399e6293d https://github.com/galaxyproject/galaxy/commit/e9f12d3b5b297b52372dbbf23a45… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- move dict formatting call from api controller to manager Commit: 6406276146715ee14a8624a18238ec40ea7c341c https://github.com/galaxyproject/galaxy/commit/6406276146715ee14a8624a18238… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- Merge pull request #806 from martenson/data-lib-work UI and API for data library folders management Compare: https://github.com/galaxyproject/galaxy/compare/531875753df5...640627614671

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[galaxyproject/galaxy] 90f63a: Tweak password reset email template to truly be pl...
by GitHub 29 Sep '15

29 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90f63a401b0c7c15dfca19f6d9f2c1546216127c https://github.com/galaxyproject/galaxy/commit/90f63a401b0c7c15dfca19f6d9f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Tweak password reset email template to truly be plain text. Commit: 531875753df5158073c4de642ba3d4046810956d https://github.com/galaxyproject/galaxy/commit/531875753df5158073c4de642ba3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #812 from dannon/prt_email_tweak Tweak password reset email template to truly be plain text. Compare: https://github.com/galaxyproject/galaxy/compare/75cc56793c21...531875753df5

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[galaxyproject/galaxy] ac18cb: Improved "special" tool loading.
by GitHub 29 Sep '15

29 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac18cbe978c72c90c9659f225a05adad653971c6 https://github.com/galaxyproject/galaxy/commit/ac18cbe978c72c90c9659f225a05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_parsing.py Log Message: ----------- Improved "special" tool loading. Instead of writing out the tools on startup (a more expensive operation than reading), just read the existing files in. Add new abstraction to the tool panel to reduce some otherwise duplicated code. Testing: The following two API tests should cover the modified behavior, they verify that metadata is still detectable and that history import and export still works. ``` ./run_tests.sh -api test/api/test_histories.py:HistoriesApiTestCase.test_import_export ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_rdata_not_decompressed ``` Commit: de2bb5771bd86d1f3f95bdce84b0e07536d27cb9 https://github.com/galaxyproject/galaxy/commit/de2bb5771bd86d1f3f95bdce84b0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove unused code. Commit: 75cc56793c21f991d15b787e0f07e9c6897e1ce4 https://github.com/galaxyproject/galaxy/commit/75cc56793c21f991d15b787e0f07… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #813 from jmchilton/tool_loading Small tweaks to tool loading. Compare: https://github.com/galaxyproject/galaxy/compare/90dc2b1093d6...75cc56793c21

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[galaxyproject/usegalaxy-playbook] 85d58d: Update Test Galaxy and Pulsar
by GitHub 29 Sep '15

29 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 85d58d667cd561fc1281fe587e9f7dd5c1b07933 https://github.com/galaxyproject/usegalaxy-playbook/commit/85d58d667cd561fc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M stage/group_vars/all.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Test Galaxy and Pulsar

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[galaxyproject/galaxy] e52b9a: Show tool parameter errors on initial tool form lo...
by GitHub 29 Sep '15

29 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e52b9ac2552ea19c6e534968661382e23cc362fa https://github.com/galaxyproject/galaxy/commit/e52b9ac2552ea19c6e5349686613… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Show tool parameter errors on initial tool form load. Needed for e.g. proper rerun display behavoir. Commit: 394c3726d6ff6d515b99361465c743d7cd9651d9 https://github.com/galaxyproject/galaxy/commit/394c3726d6ff6d515b99361465c7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge pull request #802 from blankenberg/tool_error_fixes [15.07] Show tool parameter errors on initial tool form load. Commit: 6fef4465ae3f8875a1aa6153d957941dd3fd737e https://github.com/galaxyproject/galaxy/commit/6fef4465ae3f8875a1aa6153d957… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- [Pulsar] Resubmit AMQP acknowledgement messages to the correct queue when consuming more than one. Also, only start one acknowledgement manager thread rather than one per consumer. Commit: 8c9e8686a159ec9fbee65457a8042fdcefd632f2 https://github.com/galaxyproject/galaxy/commit/8c9e8686a159ec9fbee65457a804… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge pull request #808 from natefoo/amqp_ack [15.07] [Pulsar] Resubmit AMQP acknowledgement messages to the correct queue Commit: 90dc2b1093d631bd312857b3ecb13d46fe1e0cdd https://github.com/galaxyproject/galaxy/commit/90dc2b1093d631bd312857b3ecb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M lib/pulsar/client/amqp_exchange.py M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge branch 'release_15.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3e0221c0d092...90dc2b1093d6

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[galaxyproject/galaxy] 6fef44: [Pulsar] Resubmit AMQP acknowledgement messages to...
by GitHub 29 Sep '15

29 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 6fef4465ae3f8875a1aa6153d957941dd3fd737e https://github.com/galaxyproject/galaxy/commit/6fef4465ae3f8875a1aa6153d957… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- [Pulsar] Resubmit AMQP acknowledgement messages to the correct queue when consuming more than one. Also, only start one acknowledgement manager thread rather than one per consumer. Commit: 8c9e8686a159ec9fbee65457a8042fdcefd632f2 https://github.com/galaxyproject/galaxy/commit/8c9e8686a159ec9fbee65457a804… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge pull request #808 from natefoo/amqp_ack [15.07] [Pulsar] Resubmit AMQP acknowledgement messages to the correct queue Compare: https://github.com/galaxyproject/galaxy/compare/394c3726d6ff...8c9e8686a159

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[galaxyproject/usegalaxy-playbook] 4a2dca: Updated images in slide show: Riboseq replaced Wha...
by GitHub 28 Sep '15

28 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4a2dca8323e6d9a0f72abecef31a2abaa9ade459 https://github.com/galaxyproject/usegalaxy-playbook/commit/4a2dca8323e6d9a0… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016TrNom.png A files/galaxy/common/static/welcome_img/Riboseq.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated images in slide show: Riboseq replaced Whate Shark and generic GCC2016 became topic nominations are open.

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[galaxyproject/galaxy] d3b535: Fix framework test failures.
by GitHub 28 Sep '15

28 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3b53544dffd0297f326f67757e11b153b898b3d https://github.com/galaxyproject/galaxy/commit/d3b53544dffd0297f326f67757e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Fix framework test failures. Some other fix caused the yaml example tool to load in the framework and api tests again after a long regression, this in turn caused a more recent regression to pop out in the framework test suite. This fixes that, thanks for the heads up @martenson. Commit: 3e0221c0d092f3512768c24dcb48398398f4bedf https://github.com/galaxyproject/galaxy/commit/3e0221c0d092f3512768c24dcb48… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Merge pull request #807 from jmchilton/framework_test_failures Fix framework test failures. Compare: https://github.com/galaxyproject/galaxy/compare/bd3e86c046bf...3e0221c0d092

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[galaxyproject/galaxy] e52b9a: Show tool parameter errors on initial tool form lo...
by GitHub 28 Sep '15

28 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: e52b9ac2552ea19c6e534968661382e23cc362fa https://github.com/galaxyproject/galaxy/commit/e52b9ac2552ea19c6e5349686613… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Show tool parameter errors on initial tool form load. Needed for e.g. proper rerun display behavoir. Commit: 394c3726d6ff6d515b99361465c743d7cd9651d9 https://github.com/galaxyproject/galaxy/commit/394c3726d6ff6d515b99361465c7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge pull request #802 from blankenberg/tool_error_fixes [15.07] Show tool parameter errors on initial tool form load. Compare: https://github.com/galaxyproject/galaxy/compare/1a17dbb68d23...394c3726d6ff

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[galaxyproject/galaxy] 5ff102: Add regression test for issue in #798.
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ff102507b7b461d404f5747532e21caf551ac9c https://github.com/galaxyproject/galaxy/commit/5ff102507b7b461d404f5747532e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/api/test_tools.py M test/functional/tools/validation_repeat.xml Log Message: ----------- Add regression test for issue in #798. Commit: bd3e86c046bf5609b95a7b82f0751ee97bfd637c https://github.com/galaxyproject/galaxy/commit/bd3e86c046bf5609b95a7b82f075… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/api/test_tools.py M test/functional/tools/validation_repeat.xml Log Message: ----------- Merge pull request #801 from jmchilton/validator_repeat_test Add regression test for issue in #798. Compare: https://github.com/galaxyproject/galaxy/compare/6d5ee0b6c8c2...bd3e86c046bf

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[galaxyproject/galaxy] 05f02c: Fix for not respecting tool errors when trying to ...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05f02cf9b47c551347299c1a940fc00561d2f71f https://github.com/galaxyproject/galaxy/commit/05f02cf9b47c551347299c1a940f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for not respecting tool errors when trying to execute tools where the error occurs within a repeat. Commit: 1a17dbb68d23c3ba775a654e1d03d4e131c2c4fe https://github.com/galaxyproject/galaxy/commit/1a17dbb68d23c3ba775a654e1d03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #798 from blankenberg/tool_error_fixes [15.07] Fix for not respecting tool errors when trying to execute tools Commit: 759b67dfa8cc59fb1e263d16acfeadd0ab196556 https://github.com/galaxyproject/galaxy/commit/759b67dfa8cc59fb1e263d16acfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_15.07' Commit: 6d5ee0b6c8c2eb8b343a4473e253bb14e34b1da0 https://github.com/galaxyproject/galaxy/commit/6d5ee0b6c8c2eb8b343a4473e253… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0260d753c76d...6d5ee0b6c8c2

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[galaxyproject/galaxy] 05f02c: Fix for not respecting tool errors when trying to ...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 05f02cf9b47c551347299c1a940fc00561d2f71f https://github.com/galaxyproject/galaxy/commit/05f02cf9b47c551347299c1a940f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for not respecting tool errors when trying to execute tools where the error occurs within a repeat. Commit: 1a17dbb68d23c3ba775a654e1d03d4e131c2c4fe https://github.com/galaxyproject/galaxy/commit/1a17dbb68d23c3ba775a654e1d03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #798 from blankenberg/tool_error_fixes [15.07] Fix for not respecting tool errors when trying to execute tools Commit: 759b67dfa8cc59fb1e263d16acfeadd0ab196556 https://github.com/galaxyproject/galaxy/commit/759b67dfa8cc59fb1e263d16acfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/79c58bd9250c...759b67dfa8cc

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[galaxyproject/galaxy] 05f02c: Fix for not respecting tool errors when trying to ...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 05f02cf9b47c551347299c1a940fc00561d2f71f https://github.com/galaxyproject/galaxy/commit/05f02cf9b47c551347299c1a940f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for not respecting tool errors when trying to execute tools where the error occurs within a repeat. Commit: 1a17dbb68d23c3ba775a654e1d03d4e131c2c4fe https://github.com/galaxyproject/galaxy/commit/1a17dbb68d23c3ba775a654e1d03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #798 from blankenberg/tool_error_fixes [15.07] Fix for not respecting tool errors when trying to execute tools Compare: https://github.com/galaxyproject/galaxy/compare/e00674550830...1a17dbb68d23

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[galaxyproject/galaxy] 3f3c1b: Pin IE versions
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f3c1b679bfef5dbd75d7c267d25fd2979f362d1 https://github.com/galaxyproject/galaxy/commit/3f3c1b679bfef5dbd75d7c267d25… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Pin IE versions Commit: 85df2f67c4988700232098d4dc08f2bc5148359d https://github.com/galaxyproject/galaxy/commit/85df2f67c4988700232098d4dc08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge pull request #785 from erasche/pin-gie-images [release_15.07] pin GIE image versions Commit: bf60693ed001099b78189f28d46500b572be9df7 https://github.com/galaxyproject/galaxy/commit/bf60693ed001099b78189f28d465… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: 0bf60a5205947e4e4f20090a0509474983370df7 https://github.com/galaxyproject/galaxy/commit/0bf60a5205947e4e4f20090a0509… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #794 from jmchilton/release_15.05.output.fix [15.05] Fix problem maintaining input maps when rescheduling workflows. Commit: e0067455083089dbdf35ac4b93ff94d91b689889 https://github.com/galaxyproject/galaxy/commit/e0067455083089dbdf35ac4b93ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 79c58bd9250c174ca5347bcc6cdd33f08074cecc https://github.com/galaxyproject/galaxy/commit/79c58bd9250c174ca5347bcc6cdd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.07' Commit: 0260d753c76d7305f6c1f05d08af43e61faa7641 https://github.com/galaxyproject/galaxy/commit/0260d753c76d7305f6c1f05d08af… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Log Message: ----------- Merge branch 'master' into dev Conflicts: config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Compare: https://github.com/galaxyproject/galaxy/compare/ba43e95f41c3...0260d753c76d

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[galaxyproject/galaxy] 19bc49: Binary sniffing; along with the registry forcing c...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 19bc49d207a92288dc402900cfa0125b8da45111 https://github.com/galaxyproject/galaxy/commit/19bc49d207a92288dc402900cfa0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Binary sniffing; along with the registry forcing case insensitivity through lower() which was implemented a while back, the un/sniffable formats lists should as well. This resolves #753 Commit: aff8c708a925205332c4190e3ada5712dc04519e https://github.com/galaxyproject/galaxy/commit/aff8c708a925205332c4190e3ada… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #774 from dannon/stable_sniffers [15.07] Binary sniffing; along with the registry forcing case insensitivity t… Commit: 3f3c1b679bfef5dbd75d7c267d25fd2979f362d1 https://github.com/galaxyproject/galaxy/commit/3f3c1b679bfef5dbd75d7c267d25… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Pin IE versions Commit: 85df2f67c4988700232098d4dc08f2bc5148359d https://github.com/galaxyproject/galaxy/commit/85df2f67c4988700232098d4dc08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge pull request #785 from erasche/pin-gie-images [release_15.07] pin GIE image versions Commit: bf60693ed001099b78189f28d46500b572be9df7 https://github.com/galaxyproject/galaxy/commit/bf60693ed001099b78189f28d465… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: 0bf60a5205947e4e4f20090a0509474983370df7 https://github.com/galaxyproject/galaxy/commit/0bf60a5205947e4e4f20090a0509… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #794 from jmchilton/release_15.05.output.fix [15.05] Fix problem maintaining input maps when rescheduling workflows. Commit: e0067455083089dbdf35ac4b93ff94d91b689889 https://github.com/galaxyproject/galaxy/commit/e0067455083089dbdf35ac4b93ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 79c58bd9250c174ca5347bcc6cdd33f08074cecc https://github.com/galaxyproject/galaxy/commit/79c58bd9250c174ca5347bcc6cdd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/a6715ebceccf...79c58bd9250c

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[galaxyproject/galaxy] bf6069: Fix problem maintaining input maps when rescheduli...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: bf60693ed001099b78189f28d46500b572be9df7 https://github.com/galaxyproject/galaxy/commit/bf60693ed001099b78189f28d465… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: 0bf60a5205947e4e4f20090a0509474983370df7 https://github.com/galaxyproject/galaxy/commit/0bf60a5205947e4e4f20090a0509… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #794 from jmchilton/release_15.05.output.fix [15.05] Fix problem maintaining input maps when rescheduling workflows. Commit: e0067455083089dbdf35ac4b93ff94d91b689889 https://github.com/galaxyproject/galaxy/commit/e0067455083089dbdf35ac4b93ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Compare: https://github.com/galaxyproject/galaxy/compare/85df2f67c498...e00674550830

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[galaxyproject/galaxy] bf6069: Fix problem maintaining input maps when rescheduli...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: bf60693ed001099b78189f28d46500b572be9df7 https://github.com/galaxyproject/galaxy/commit/bf60693ed001099b78189f28d465… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: 0bf60a5205947e4e4f20090a0509474983370df7 https://github.com/galaxyproject/galaxy/commit/0bf60a5205947e4e4f20090a0509… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #794 from jmchilton/release_15.05.output.fix [15.05] Fix problem maintaining input maps when rescheduling workflows. Compare: https://github.com/galaxyproject/galaxy/compare/6827aed9efb3...0bf60a520594

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[galaxyproject/galaxy] ac8b5e: Fix errors when starting "./run_tests.sh -with_fra...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac8b5eae02155a7364e4131ba88d983c69bd000b https://github.com/galaxyproject/galaxy/commit/ac8b5eae02155a7364e4131ba88d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix errors when starting "./run_tests.sh -with_framework_test_tools -api" Commit: ba43e95f41c3220df05aac0be7bc117c6acda362 https://github.com/galaxyproject/galaxy/commit/ba43e95f41c3220df05aac0be7bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #800 from nsoranzo/functional_tests_fixes Fix errors when starting "./run_tests.sh -with_framework_test_tools -api" Compare: https://github.com/galaxyproject/galaxy/compare/3f91a9a38186...ba43e95f41c3

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[galaxyproject/galaxy] 3fcf32: Add sentry configuration option and doc to galaxy....
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3fcf3210462a64ca3112295926240d04a99f3d24 https://github.com/galaxyproject/galaxy/commit/3fcf3210462a64ca311229592624… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add sentry configuration option and doc to galaxy.ini.sample Commit: 3f91a9a381868910a1f5d3e8daf784dc960ffded https://github.com/galaxyproject/galaxy/commit/3f91a9a381868910a1f5d3e8daf7… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #799 from dannon/sample_sentry Add sentry configuration option and doc to galaxy.ini.sample Compare: https://github.com/galaxyproject/galaxy/compare/a5610d6845f4...3f91a9a38186

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[galaxyproject/galaxy] 86c426: Fix unit tests broken with f935d27bdfb4ff66e841de2...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 86c4263b344f1bdd3c316a579a30f157f88eadf7 https://github.com/galaxyproject/galaxy/commit/86c4263b344f1bdd3c316a579a30… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/unit/jobs/test_job_configuration.py Log Message: ----------- Fix unit tests broken with f935d27bdfb4ff66e841de2667a40d3d65c0175d. Commit: a5610d6845f4bf016a0ac6a9a2d3d17a11e9b83b https://github.com/galaxyproject/galaxy/commit/a5610d6845f4bf016a0ac6a9a2d3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #797 from jmchilton/java_opts_doc Fix unit tests broken with f935d27bdfb4ff66e841de2667a40d3d65c0175d. Compare: https://github.com/galaxyproject/galaxy/compare/6d3ea7ee0086...a5610d6845f4

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[galaxyproject/galaxy] 484578: Refactor to use -P
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 484578936bc7ee04c6b28cb848772a4b6ded2b03 https://github.com/galaxyproject/galaxy/commit/484578936bc7ee04c6b28cb84877… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Refactor to use -P This is a major refactoring to use the -P option of docker which should simplify some of our deployment like running docker containers on another host. In support of #372 Commit: 04c5e6864cc77fa1952d1acd88bac5df93f5ac44 https://github.com/galaxyproject/galaxy/commit/04c5e6864cc77fa1952d1acd88ba… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'gie-docker-cmd' into gie-docker-launch Commit: c9e9c95514e50f9a260b5ed342a715d2846fd4fe https://github.com/galaxyproject/galaxy/commit/c9e9c95514e50f9a260b5ed342a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Correct small logic bugs, add logging Commit: a02df53f3356a03f3784070a4c50accfbc00187f https://github.com/galaxyproject/galaxy/commit/a02df53f3356a03f3784070a4c50… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako Log Message: ----------- Correct IPython notebooks to new URL Commit: a5b296b8ecd262d58a17049f5a9aeeecb7649621 https://github.com/galaxyproject/galaxy/commit/a5b296b8ecd262d58a17049f5a9a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Include user email Fixes bgruening/docker-ipython-notebook#51 Commit: a76ba39321e71cab8a0ecd3a610bcd861827815c https://github.com/galaxyproject/galaxy/commit/a76ba39321e71cab8a0ecd3a610b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Update against gie-docker-cmd Commit: 06a67c8c109dcf59425b53b80dcb5419f5e814af https://github.com/galaxyproject/galaxy/commit/06a67c8c109dcf59425b53b80dcb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Add dynamic_proxy_prefix configuration Normally the proxy binds to :8800 and runs containers under :8800/ipython/... which is great... until you have an upstream proxy like apache wrapping that at the url FQDN/ipython and suddenly your cookies aren't available because they're specific to /galaxy. Thus, when an upstream proxy is in use, we correct the proxy's path to: with :8800/{cookie_path}/gie_proxy/ipython/... which behaves much more nicely with upstraem proxies. Commit: 5a2b1ec322f0808ba4e7925effe87a467f6b467a https://github.com/galaxyproject/galaxy/commit/5a2b1ec322f0808ba4e7925effe8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'gie-docker-cmd' into gie-docker-launch Commit: 1d78033625259bc50413393422feab38116b8884 https://github.com/galaxyproject/galaxy/commit/1d78033625259bc50413393422fe… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge branch 'gie-docker-cmd' into gie-docker-launch Commit: b4bbd1c2f161959fabdb62962aa63fb630c1ca2d https://github.com/galaxyproject/galaxy/commit/b4bbd1c2f161959fabdb62962aa6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Make use of proxy path in appropriate places Commit: 4a4a7ca51b195ac9d9a718448d65c89c02ae118c https://github.com/galaxyproject/galaxy/commit/4a4a7ca51b195ac9d9a718448d65… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Update URLs for rstudio Commit: e8eb46b65d76a2b7645aa325e321d135df02e802 https://github.com/galaxyproject/galaxy/commit/e8eb46b65d76a2b7645aa325e321… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Use a backport for check_output that is not part of python 2.6 Commit: d4d439f51ebd2343e111d912499f336778e590c5 https://github.com/galaxyproject/galaxy/commit/d4d439f51ebd2343e111d912499f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #10 from erasche/check_output_backport Use a backport for check_output that is not part of python 2.6 Commit: 5f15b0d94c4a9703315f96fe3ce63b9b3906ea84 https://github.com/galaxyproject/galaxy/commit/5f15b0d94c4a9703315f96fe3ce6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Replace backported one with just the code used Sorry bjoern, ripped out what you'd added and just used the code because the doctest was failing for some unknown reason and we didn't ever need to reuse the function, so ... easier this way Commit: 6d3ea7ee0086707bbf3f6d54cfa0ee1e2221341c https://github.com/galaxyproject/galaxy/commit/6d3ea7ee0086707bbf3f6d54cfa0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/galaxy.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge pull request #790 from erasche/gie-docker-launch Refactor GIE Launching to use -P Compare: https://github.com/galaxyproject/galaxy/compare/0fefff07b34c...6d3ea7ee0086

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[galaxyproject/galaxy] f935d2: Fix _JAVA_OPTIONS example in job_conf.xml.
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f935d27bdfb4ff66e841de2667a40d3d65c0175d https://github.com/galaxyproject/galaxy/commit/f935d27bdfb4ff66e841de2667a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fix _JAVA_OPTIONS example in job_conf.xml. Thanks detailed bug report by Damion Dooley (http://dev.list.galaxyproject.org/JAVA-OPTIONS-config-parameter-in-job-conf…) Commit: 0fefff07b34c2b16793a3ae1c68849119abfa244 https://github.com/galaxyproject/galaxy/commit/0fefff07b34c2b16793a3ae1c688… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Merge pull request #796 from jmchilton/java_opts_doc Fix _JAVA_OPTIONS example in job_conf.xml.sample_advanced Compare: https://github.com/galaxyproject/galaxy/compare/0428de04fba3...0fefff07b34c

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